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churchlab
/
millstone
Genome engineering and analysis software
http://churchlab.github.io/millstone/
MIT License
47
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19
forks
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SnpEff appears to break if no features in Genbank
#663
glebkuznetsov
opened
8 years ago
0
Can't use upload form for upload from location on server for single end reads
#662
mnapolitano89
opened
8 years ago
0
Single sample upload should show progress. Can be solved by using the batch upload js component.
#661
glebkuznetsov
opened
8 years ago
0
Update documentation with list of anayze view key/descriptions
#660
glebkuznetsov
opened
8 years ago
0
Allow batch download of .bam files
#659
glebkuznetsov
opened
8 years ago
0
Loading contig view is slow, and sometimes contigs appear after user switches to Variants view
#658
glebkuznetsov
closed
8 years ago
0
No long alts in db. Store and fetch from file instead.
#657
glebkuznetsov
closed
8 years ago
0
Mobile element detection finishing
#656
woodymit
closed
8 years ago
0
Don't write ref_value > 10 bases to database.
#655
glebkuznetsov
closed
8 years ago
2
List multiple affected genes when applicable (e.g. for large deletions).
#654
dbgoodman
opened
8 years ago
0
Update readthedocs with 'Quick Start' section
#653
glebkuznetsov
opened
8 years ago
0
Use mobile element features rebase
#652
woodymit
closed
8 years ago
0
Alignment fails if Genbank has name like `geneious|urn:loc`
#651
glebkuznetsov
opened
8 years ago
0
If one of the SV callers fail, the whole pipeline shows an error even though variant calling worked for other parts
#650
glebkuznetsov
opened
8 years ago
0
Update SnpEff to latest version (4.3)
#649
glebkuznetsov
closed
8 years ago
0
New version of SnpEff can give list of predicted effects for a single alt
#648
glebkuznetsov
opened
8 years ago
0
Hook all the different variant calling methods (LUMPY, PINDEL, GRAPHWALK, COVERAGE) into the alignment options UI.
#647
dbgoodman
opened
8 years ago
0
FREEBAYES_PARALLEL misses variants if multiple chromosomes
#646
glebkuznetsov
closed
8 years ago
0
Jbrowsing contigs with extracted read alignment fails to render bam track on AWS
#645
woodymit
opened
8 years ago
1
Alignment to totally mismtached FASTQ gives error at compute_insert_metrics()
#644
glebkuznetsov
closed
8 years ago
0
Can't support ReferenceGenome with non-ascii character in the name
#643
glebkuznetsov
closed
8 years ago
1
Need to show alignment stats somewhere (e.g. % reads aligned, etc.)
#642
glebkuznetsov
opened
8 years ago
0
SnpEff Error if no variants called
#641
glebkuznetsov
opened
8 years ago
0
Custom reference genome exported from Geneious causes SnpEff error
#640
glebkuznetsov
closed
8 years ago
4
Github README needs more specific information about what the package does
#639
glebkuznetsov
opened
8 years ago
0
SAMPLE not recognized key. Only EXPERIMENT_SAMPLE_LABEL. Should make this work.
#638
glebkuznetsov
closed
8 years ago
0
Deletions found by COVERAGE don't show up in analyze view for IS_SV = True Ftiler
#637
glebkuznetsov
closed
8 years ago
1
Altalign deletion detect rebase
#636
woodymit
closed
8 years ago
0
Added Error message and blank effect for missing EFF INFO fields
#635
dbgoodman
closed
8 years ago
0
Links to Melted View do not work properly if you have multiple AlignmentGroups.
#634
dbgoodman
opened
8 years ago
0
While aligning, ExperimentSamples should not say READY while VARIANT_CALLING is still running
#633
glebkuznetsov
opened
8 years ago
0
Filter contigs
#632
woodymit
closed
8 years ago
0
Dataset.filesystem_idx_location used inconsistently
#631
woodymit
closed
8 years ago
3
Update celery workers automatically on machine resize
#630
glebkuznetsov
opened
8 years ago
0
Running FASTQC on imported samples is super slow
#629
glebkuznetsov
opened
8 years ago
3
Parallel contig assembly
#628
woodymit
closed
8 years ago
3
Parallelize contig assembly on multiple samples
#627
glebkuznetsov
closed
8 years ago
1
Graph walk detect translocation
#626
woodymit
closed
8 years ago
2
Test basic callable loci
#625
woodymit
closed
8 years ago
1
Deleting a big Project from the ui fails
#624
glebkuznetsov
opened
8 years ago
0
Graph sv discover
#623
woodymit
closed
8 years ago
0
Pindel: Error when running SnpEff
#622
glebkuznetsov
opened
8 years ago
0
Fixes for bugs discovered by DBG
#621
woodymit
closed
8 years ago
0
Contig BAM tracks are blank
#620
dbgoodman
closed
8 years ago
0
Error when deleting all contigs
#619
dbgoodman
closed
8 years ago
0
Fix 617: division by zero error in find insertion location
#618
woodymit
closed
8 years ago
0
Divide by zero error during 'Find Insertion Location'
#617
dbgoodman
closed
8 years ago
4
Fixed bug in reverse complement assembly detection
#616
woodymit
closed
8 years ago
1
Display multiple potential endpoints for contig w/JBrowse links
#615
woodymit
closed
8 years ago
0
Show sv junctions
#614
woodymit
closed
8 years ago
1
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